By the way, we have many other cool deployment-related features on our roadmap, so please track progress and submit your feedback and new ideas in YouTrack , our fastest issue tracker for Web IDE project.

Ainu, actually, you can choose which files to upload: just select an individual file(s) and/or folder(s) in the Project view and invoke Upload context menu action. We also plan to allow one upload the items from the VCS changelist manually and automatically on commit (http://youtrack.jetbrains.net/issue/WI-421).